The Indonesian defence minister has warned other countries to respect his country’s sovereignty over the troubled region of Papua, as meetings with Australian ministers ended in mutual agreement about the strength of the bilateral relationship.

Ryamizard Ryacudu said Indonesia had “never disrupted or caused disruptions in other countries” and it expected the same of other nations regarding Papua and its long-running independence movement.

“There are countries that are getting involved in the issue of Papua. For us, Papua is [part] of the united Republic of Indonesia. The united Republic of Indonesia extends from Sabang [in Sumatra] to Papua. There is no other solution, that’s it, that’s the way it is,” Ryacudu said in Sydney on Monday.

The comments from Ryacudu, who previously served as chief of staff of the Indonesian Army (TNI) and commander of the Strategic Army Command, or Kostrad, follow reports that all international NGOs have been ordered to close offices in Papua.

Ryacudu, who previously served as chief of staff of the Indonesian army (TNI) and commander of the strategic army command, was in Sydney with foreign minister Retno Marsudi for a meeting with Australian foreign minister Julie Bishop and defence minister Marise Payne.

Bishop confirmed Papua was discussed during the talks and reiterated that Australia respected Indonesia’s sovereignty over Papua.

“On the issue of Papua, yes, that was part of our discussions. We had a general discussion about regional issues, about Pacific issues and Australia restated, as we have done on many occasions, publicly and privately, our unconditional support and respect for Indonesia’s sovereignty in this regard,” Bishop said.

Indonesia, which took control of Papua from the Dutch in 1963, has for a long time fought a separatist movement in the province and faced various allegations of systematic abuse of Papuans.

The Indonesian military has been accused of numerous human rights abuses, while the local population complains that much of the wealth generated in the resource-rich province flows back to Jakarta while West Papuans remain poor.

After the meetings, Bishop said relations between the nations were in very good shape. Relations with Indonesia might have been frosty following the Bali Nine executions, but Bishop said there had been 15 ministerial meetings between the countries since August.

Monday’s meeting focused on national security, including counter-terrorism, deradicalisation and intelligence-sharing, as well as economic ties, she told reporters after the meeting.

Australia and Indonesia were close neighbours and natural partners, Bishop said.

As well as security and economic ties, there were growing links in tourism and student exchange.

“We have shared and common interests across a broad and diverse range of areas,” Bishop said. “There is room for us as two G20 economies to do a great deal more together.”

Indonesian foreign minister Retno Marsudi agreed the relationship between Jakarta and Canberra was in good shape, especially after Malcolm Turnbull’s visit to Jakarta.

The touchy issue of people smuggling and Australia’s boat turnback policy was the subject of a “very frank and honest discussion”, Bishop said.

Marsudi said both nations would continue to cooperate on addressing the root causes of people smuggling.

Ryacudu said real threats facing the region included terrorism, natural disaster, disease, drug smuggling and the “hassle” of refugees.